Success of the shrimp aquaculture industry requires technological advances that increase production and environmental sustainability. Indoor, superintensive, aquaculture systems have been developed that permit year-round production of farmed shrimp at high densities. These systems overcome problems of lower growth rates, disease susceptibility, and water quality issues from waste products by operating as essentially closed systems that promote beneficial microbial communities (biofloc). The resulting biofloc assimilates and detoxifies wastes, provides nutrition for the farmed organisms resulting in improved growth, and reduces disease initiated from external sources. NMR-based metabolomic techniques were used to assess shrimp health during a full growout cycle from the nursery phase through harvest in a minimal-exchange, superintensive, biofloc system. Metabolomics techniques detected aberrant shrimp metabolomes from a spike in total ammonia nitrogen in the nursery, from a reduced feeding period that was a consequence of surface scum build-up in the raceway, and from the stocking transition from the nursery to the growout raceway. The biochemical changes induced by the stressors were essential for survival and included nitrogen detoxification and energy conservation mechanisms. Inosine and trehalose may be general biomarkers of stress in Litopenaeus vannamei. This study demonstrates one aspect of the practicality of using NMR-based metabolomics to enhance the aquaculture industry.